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List:       bioc-devel
Subject:    Re: [Bioc-devel] AnnotationHub: uniprot seqs ?
From:       "Liu, Haibo" <Haibo.Liu () umassmed ! edu>
Date:       2024-05-21 13:26:27
Message-ID: CH3PR10MB750485509AB5B78182CD63E186EA2 () CH3PR10MB7504 ! namprd10 ! prod ! outlook ! com
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If you have many sequences to download, it can be very slow if you use Uniprot.ws to \
query the database. I used a walk-around method to download the proteome of a species \
using FTP in my dagLogo package: \
https://github.com/jianhong/dagLogo/blob/devel/R/prepareProteomeByFTP.R.

Haibo

-----Original Message-----
From: aditya.bhagwat@uni-marburg.de <aditya.bhagwat@uni-marburg.de>
Sent: Tuesday, May 21, 2024 9:20 AM
To: Liu, Haibo <Haibo.Liu@umassmed.edu>
Cc: Vincent Carey <stvjc@channing.harvard.edu>; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] AnnotationHub: uniprot seqs ?

Thank you Haibo and Vincent : )

Yes, UniProt.ws is certainly there and did serve me well earlier.
There are times when an offline solution is needed, when operations are done on \
larger sets. Followed my habit to check first whether a relevant AnnotationHub record \
exists. Given the absence of that, I downloaded the relevant fastafile manually from \
UniProt. Read it in with Biostrings and then took it from there.
Which is quite hassle-free, so yes, I can see that there is no need and not much \
value to pull it into AnnotationHub. Thankyou for sharing your experience : )

Cheers,

Aditya




> We use Uniprot.ws to access the Uniprot data on demand:
> https://bioconductor.org/packages/release/bioc/html/UniProt.ws.html.
> 
> Haibo
> 
> -----Original Message-----
> From: Bioc-devel <bioc-devel-bounces@r-project.org> On Behalf Of
> Vincent Carey
> Sent: Tuesday, May 21, 2024 7:02 AM
> To: aditya.bhagwat@uni-marburg.de
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] AnnotationHub: uniprot seqs ?
> 
> On Tue, May 21, 2024 at 4:18 AM Aditya Bhagwat via Bioc-devel <
> bioc-devel@r-project.org> wrote:
> 
> > Hey guys,
> > 
> > Do we have Uniprot sequences in AnnotationHub ?
> > 
> 
> That does not seem practical.
> 
> Please see
> https://bioconductor.org/packages/release/bioc/vignettes/UniProt.ws/inst/doc/UniProt.ws.html
>  
> Let us know if that does not meet your need.
> 
> 
> > Not being able to find them.
> > 
> 
> 
> 
> > 
> > Thankyouverymuch : )
> > 
> > Aditya
> > 
> > --
> > Aditya Bhagwat
> > Translational Proteomics ∙ Philipps-University Marburg
> > 
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
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> > umassmed.edu%7C47f0c877418b4558bdac08dc79859dee%7Cee9155fe2da34378a6c4
> > 4405faf57b2e%7C0%7C0%7C638518862010686203%7CUnknown%7CTWFpbGZsb3d8eyJW
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> 
> --
> The information in this email is intended only for the p...{{dropped:15}}
> 
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--
Aditya Bhagwat
Translational Proteomics ∙ Philipps-University Marburg
Biological Pharmacological Center ∙ Room A406
Tel.: +49 6421 28 27403

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